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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "spacexr" in publications use:'
type: software
license: GPL-3.0-or-later
title: 'spacexr: SpatialeXpressionR: Cell Type Identification in Spatial Transcriptomics'
version: 1.5.0
doi: 10.1038/s41587-021-00830-w
identifiers:
- type: doi
  value: 10.32614/CRAN.package.spacexr
abstract: 'Spatial-eXpression-R (spacexr) is a package for analyzing cell types in
  spatial transcriptomics data. This implementation is a fork of the spacexr GitHub
  repo (https://github.com/dmcable/spacexr), adapted to work with Bioconductor objects.
  The original package implements two statistical methods: RCTD for learning cell
  types and CSIDE for inferring cell type-specific differential expression. Currently,
  this fork only implements RCTD, which learns cell type profiles from annotated RNA
  sequencing (RNA-seq) reference data and uses these profiles to identify cell types
  in spatial transcriptomic pixels while accounting for platform-specific effects.
  Future releases will include an implementation of CSIDE.'
authors:
- family-names: Cable
  given-names: Dylan
  email: dmcable@umich.edu
- family-names: Irizarry
  given-names: Rafael
  email: rafael_irizarry@dfci.harvard.edu
  orcid: https://orcid.org/0000-0002-3944-4309
- family-names: Grajeda
  given-names: Gabriel
  email: gabriel.grajeda@gmail.com
  orcid: https://orcid.org/0009-0003-7242-7476
preferred-citation:
  type: article
  title: Robust decomposition of cell type mixtures in spatial transcriptomics
  authors:
  - family-names: Cable
    given-names: Dylan M.
  - family-names: Murray
    given-names: Evan
  - family-names: Zou
    given-names: Luli S.
  - family-names: Goeva
    given-names: Aleksandrina
  - family-names: Macosko
    given-names: Evan Z.
  - family-names: Chen
    given-names: Fei
  - family-names: Irizarry
    given-names: Rafael A.
  journal: Nature Biotechnology
  year: '2022'
  volume: '40'
  issue: '4'
  doi: 10.1038/s41587-021-00830-w
  start: '517'
repository: https://bioc.r-universe.dev
repository-code: https://github.com/ggrajeda/spacexr
commit: b981b934b5bb557afd4f60a38deacf80acfcfa9d
url: https://github.com/ggrajeda/spacexr
date-released: '2026-04-28'
contact:
- family-names: Grajeda
  given-names: Gabriel
  email: gabriel.grajeda@gmail.com
  orcid: https://orcid.org/0009-0003-7242-7476